RetrogeneDB ID: retro_dnov_775

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_10619:56623..57027(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSDNOG00000024843
• Aliases: None
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_dnov_775
ATGGCCCAAACCAAGCAGACTGCTCGTAAATCCACTGGTGGGAAAGCTCCCCGCAAACAGCTGGCCACTAAGGCTGCCCG
GAAAAGCGCCCCCTCTACCGGCGGGGCGAAGAAACCCCATCGTTCCAGGCCTGGAACTTTGTGCTTCGAGAGACTCGTCG
CTACCAGAAATCCACCGAGCTTCTGATCCGGAAGCTGCCTTTCAGAGGTTGGGGAGGGAGGTCGCCCAGGACGTCAGAAC
TGACTGGAGGTTTCAGAGCGCGGCATTGGCGCGCTTCAGGAGCCAGCGGAGCGTGCCTGGTGGGTTTATTTGAAGATGCT
AATCTCTGTCCCATTCATGCTAAGAGAGTCACCATCATGCCCAGAGACATCCAGTTGGCTCGTGAGATGCGCGGAGAGAG
AGCT

Alignment

ORF - retro_dnov_775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTV-ALREIRRYQKSTELLIRKLP-F
          MA.TKQTARKSTGGKAPRKQLATKAARKSAPSTGG.KKPHR.RPGT...LRE.RRYQKSTELLIRKLP.F
Retrocopy MAQTKQTARKSTGGKAPRKQLATKAARKSAPSTGGAKKPHRSRPGTL<VLRETRRYQKSTELLIRKLP<F

Parental  QRLVREIAQDFKTDLRFQSAA-IGALQE-ASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          QRL.RE.AQD..TD.RFQSAA.IGALQE.AS.A.LVGLFED.NLC.IHAKRVTIMP.DIQLAR..RGERA
Retrocopy QRLGREVAQDVRTDWRFQSAA<IGALQE<ASGACLVGLFEDANLCPIHAKRVTIMPRDIQLAREMRGERA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	379.21 RPM
SRP012922_cerebellum	0.00 RPM	285.66 RPM
SRP012922_heart	0.00 RPM	37.36 RPM
SRP012922_kidney	0.00 RPM	136.90 RPM
SRP012922_liver	0.00 RPM	169.05 RPM
SRP012922_lung	0.00 RPM	393.88 RPM
SRP012922_quadricep_muscle	0.00 RPM	46.91 RPM
SRP012922_spleen	0.00 RPM	426.60 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_775 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775 ,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,